SMILES Tutorial: Reactions

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Reaction specification

Reactions are indicated in SMILES by specifying reactant, agent and product molecule(s) separated by the "greater-than" symbol ('>'). Multiple molecules per role may be specified by use of the dot disconnections. For most purposes, SMILES reaction do not need to be stoichiometrically balanced nor that net charge is preserved (in general, both are recommended).

Isotopic specifications in SMILES.
Depiction SMILES and remark

combustion of methane (stoichiometric)


life ... don't talk to me about life


nitration of propane to form various products (non-stoichimetric representation)


esterification of acetic acid and ethanol to ethyl acetate


SN2 backside displacement of cis-3-methylcyclopentylchloride to the trans alcohol.

Atom mapping

SMILES atom maps allow specification of which reactant atoms correspond to atoms in products (i.e., the mechanism). Reaction atom mapping is never absolutely required, although it is very useful for controlling transformation mechanisms and for searching atom-mapped databases. Atom maps are numbers which represent classes and are normally paired (i.e., one reactant and one product atom have the same map-class). It is possible to give many atoms the same map class (e.g., when atoms are equivalent on both sides). Atoms in agent molecules are never given atom maps. Atom maps are treated as isomeric features (also: agents).

The following SMILES represents a stoichiometrically complete specification of the acid catalyzed esterification of acetic acid and ethanol to ethyl acetate and water. Note that [H+] is indicated as an agent. The atom-mapping of the oxygens specifies that it is the carboxy oxygen which becomes water and that the alcohol oxygen becomes the ester oxygen.


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